"Every publisher should have a publishing workflow." There is nothing novel about that. There is a base format (for the publisher) from which all publications are born. EPUB 3 is a candidate. Or something more general involving HTML5, XML, any combination of these with CSS and JS, etc.

The publisher might have their own EPUB with some additions (e.g. Apple's fixed-layout EPUB). The point is the base format is fixed, and from the base format all other formats flow. I'll just call the publisher's own base format EPUB Me, and the file extension .epme (though it might just be .epub following the appropriate specification).

There are various channels the publisher distributes through. These will likely require a conversion from EPUB Me to another format. Take Amazon's KF8 as an example. Thankfully, Amazon has provided a document and a tool for enabling the publisher to covert EPUB Me to KF8. The publisher first has to convert — how this is done is technology adopted or developed by the publisher — their own .epme to a .epub+ that KindleGen can accept. (That's where the document comes in: to define what type of HTML+CSS Amazon will accept either in .epub form or a directory of HTML+CSS+image files.) KindleGen will output .kf8.

Apple's format is not so simple: How do you go from .epme to .ibooks? Given the restrictions of iBooks Author, one way would be to use an EPUB to DOC converter (EPUBtoDOC*, or E2D for short), import the DOC file into iBooks Author, and edit (hopefully without a lot of work) what is there to make it right for delivery in the Apple channel.

The key to this workflow is that the original source.epmebelongs to the publisher alone and not to the channel on which it's distributed. output.ibooks may be "owned" by Apple, but source.epme is owned by the publisher.

iBooks Author seems pretty much like a black hole though. One might manage somehow to get EPUB in, but one can't get anything useful, like EPUB 3 (other than Apple's proprietary format), out.

I.e.: From authors/publishers point of view, they need to feed into the Apple .ibooks format if that turns out to be useful for them, but keep their original source (their .epme) separate, so they can feed that same source independently into different channels as well.

This workflow model can be extended to any number of distribution channels.